Life: conserved ion and amino acid transporters

By: James V. Kohl | Published on: April 2, 2015

The vital question: Why is life the way it is?

Excerpt: “…any sufficiently advanced chemiosmotic geochemistry is indistinguishable from life.”
My comment: If the differences between viruses and cellular life are removed, the link from viral microRNAs to the anti-entropic epigenetic effects of nutrient-dependent microRNAs limits explanations of how the nutrient-dependent microRNA/messenger RNA balance leads to the pheromone-controlled biodiversity of species from microbes to humans via RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all animal species.
See for example: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit
Excerpt: “The integration of sensory information with network states may represent a general mechanism for generating variability in behavior.”
My comment: The variability in behavior exemplified in C. elegans and P. pacificus is clearly due to dietary differences.
See also: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes reported as: The neurobiological consequence of predating or grazing
Excerpt: “The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes.”
See also: Conserved ion and amino acid transporters identified as phosphorylcholine-modified N-glycoproteins by metabolic labeling with propargylcholine in Caenorhabditis elegans cells
Excerpt: Several identified PC-proteins are nematode-specific proteins, but 10 of the PC-proteins are widely conserved ion transporters and amino acid transporters, while eight are conserved proteins involved in synaptic function. This finding suggests a functional role for PC-modification beyond immunomodulation.
See also: On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.
My comment: The link from non-living viruses to cellular life appears to be chemiosmotic geochemistry via the “…widely conserved ion transporters and amino acid transporters…”
Hopefully, in his new book,  Nick Lane will not ignore the need to link abiotic geochemistry to chemiosmotic geochemistry before proceeding to tell us “Why Life Is the Way it Is.”
His past publications include: 1) Energy at life’s origin and 2) A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria. They do not include any link to life from the sun’s biological energy.
1) Excerpt: “Research on the origin of life has long focused on chemical synthesis and the RNA world, neither of which pointed to specific early-Earth environments or specific groups of organisms as ancient.”
2) Excerpt: ” We support our inferences with comparative biochemistry and phylogenetics, and show why the late evolution of modern membranes forced divergence in other traits such as DNA replication.”
My comment: I support my model of ecological variation that leads from the de novo creation of light-induced amino acid substitutions to cell type differentiation in all genera with facts.  See for example:
1) Origin-of-life puzzle cracked
Excerpt: “Sutherland’s team now reports that it created nucleic acid precursors starting with just hydrogen cyanide (HCN), hydrogen sulfide (H2S), and ultraviolet (UV) light. What is more, Sutherland says, the same conditions also create the starting materials for amino acids and lipids.”
2) Discovery Demystifies Origin Of Life Phenomenon
Excerpt: Tianbo Liu has discovered that Mother Nature’s clear bias toward certain amino acids and sugars and against others isn’t accidental.
3) Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Excerpt: There is intense interest in determining whether coherent quantum processes play a nontrivial role in biology. This interest was sparked by the discovery of long-lived oscillations in 2D electronic spectra of photosynthetic proteins, including the phycobiliproteins (PBPs) from cryptophyte algae. Using X-ray crystallography, we show that cryptophyte PBPs adopt one of two quaternary structures, open or closed. The key feature of the closed form is the juxtaposition of two central chromophores resulting in excitonic coupling. The switch between forms is ascribed to the insertion of a single amino acid in the open-form proteins.
My comment: In my model, the change in a single amino acid substitution links the virulence of viruses from viral microRNAs and anti-entropic nutrient-dependent microRNAs to RNA-mediated cell type differentiation in all genera via their physiology of nutrient-dependent reproduction, which fixes the amino acid substitutions in the organized genomes of all genera.
The physiology of nutrient-dependent reproduction also enables the entropic elasticity, which is required for ecological variation to lead to ecological adaptation in ever-changing ecologies linked to biodiversity.
Anyone who believes that “…any sufficiently advanced chemiosmotic geochemistry is indistinguishable from life” probably is not aware of the link from the sun’s biological energy to live and may even think that life somehow “evolved” in a “warm little pond” or arrived on Earth from its deep space origin.


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